A computer system is operable to store a plurality of setting variables associated with booting configurations of system elements of the computer system, such as a total number of central processing units, a total number of memories and so forth. A value of each of the setting variables may be changed according to the change of settings by the user. However, when at least one of the values of the setting variables is not properly set or is tampered with by a testing tool, malicious software, a beta version Basic Input/Output System (BIOS) or a computer virus at an early stage of a booting process of the computer system, that is to say, before a user is allowed to enter a BIOS setup menu for changing the setting variables, it is impossible to know which one(s) of the setting variables has an improper value or a value that has been tampered with at the early stage of the booting process of the computer system. When the setting variables having the improper values are used for system configuration during the booting process of the computer system, malfunction or crash of the computer system may be caused.